That is a nasty issue with paragraphs that are set to span columns, and apparently it works like that by design (no idea what was Adobe's logic with that).
The only fix that i know of is to fake it. Move the footnote marker in the two-columns part of the text, hide it (by applying to it a 0.1pt, NoFill character style), and in the one column part of the text, where the footnote should be, just write "10" and apply superscript (or whatever footnote marker formating you are using)
I have followed the same procedure for the below issue. Because the document have more than 150 foot notes.
Also i have searched forum and i couldn't find any answer.
I expecting solution from adobe for this issue.
Don't hold your breath waiting for an answer from adobe (btw, have you filed a bugreport for this? Feature Request/Bug Report Form)
Creating an automated solution for this might be possible, but i'm guessing that out of 150 footnotes not many of them exhibit this problem, so fixing them by hand might be faster.
Query flagged.Any update from adobe staff.